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Term	Abbreviation	Description
Mitochondrial marker enzymes		Mitochondrial marker enzymes are enzymes that are specifically present in mitochondria, in the mt-matrix, the inner mt-membrane, the inter-membrane space, or the outer mt-membrane.
Monoamine oxidase	MAO	Monoamine oxidases are enzymes bound to the outer membrane of mitochondria and they catalyze the oxidative deamination of monoamines. Oxygen is used to remove an amine group from a molecule, resulting in the corresponding aldehyde and ammonia. Monoamine oxidases contain the covalently bound cofactor FAD and are, thus, classified as flavoproteins.
Nagarse		Nagarse is a broad specifity protease from bacteria used to promote breakdown of the cellular structure of "hard" tissues such as skeletal muscle or heart mucsle that cannot be homogenized easily without treatment with a protease. Nagarse is frequently used in protocols for isolating mitochondria from muscle tissue.
Nitric oxide synthase	NOS	Nitric oxide synthase, NOS, catalyzes the production of nitric oxide (NO•), which is a reactive nitrogen species. There are four types of NOS: neuronal NOS (nNOS), endothelial NOS (eNOS), inducible NOS (iNOS) and mitochondrial NOS (mtNOS).
Oxoglutarate dehydrogenase	OgDH	Oxoglutarate dehydrogenase (α-ketoglutarate dehydrogenase) is a highly regulated enzyme of the tricarboxylic acid cycle. It catalyses the conversion of oxoglutarate (alpha-ketoglutarate) to succinyl-CoA, reduces NAD⁺ to NADH and thus links to Complex I in the Electron transfer-pathway. OgDH is activated by low Ca²⁺ (<20 µM) but inactivated by high Ca²⁺ (>100 µM). OgDH is an important source of ROS.
Phosphate carrier	PiC	The phosphate carrier (PiC) is a proton/phosphate symporter which transports negatively charged inorganic phosphate across the inner mt-membrane. The transport can be described either as symport of H⁺ with P_i, or antiport of hydroxide anion against P_i. The phosphate carrier is a component of the phosphorylation system.
Phosphoenolpyruvate carboxykinase	PEPCK	Phosphoenolpyruvate carboxykinase (PEPCK) catalyzes the anabolic reaction of oxaloacetate (Oxa) to phosphoenolpyruvate at the expense of GTP. PEPCK is a cytoplasmatic enzyme involved in gluconeogenesis in mouse and rat liver, but 'is found in the mitochondria in the rabbit and chicken, and in both cytoplasm and mitochondria in the guinea pig' (Lehninger 1970). In many anoxia-resistant animals, PEPCK plays an important catabolic role under severe hypoxia and anoxia at the PEPCK branchpoint (Hochachka, Somero 2002), feeding malate into the reversed TCA cycle: malate is dismutated to pyruvate catalyzed by malic enzyme in the oxidative direction, and to fumarate in the reductive direction, leading to formation of succinate and ATP under anoxia (Gnaiger 1977).
Phosphorylation pathway	DT	From Gnaiger 2014 MitoPathways The phosphorylation pathway (phosphorylation system) is the functional unit utilizing the protonmotive force to phosphorylate ADP (D) to ATP (T), and may be defined more specifically as the P»-system. The P»-system consists of adenine nucleotide translocase, phosphate carrier, and ATP synthase. Mitochondrial adenylate kinase, mt-creatine kinase and mt-hexokinase constitute extended components of the P»-system, controlling local AMP and ADP concentrations and forming metabolic channels. Since substrate-level phosphorylation is involved in the TCA-cycle, the P»-system includes succinyl-CoA ligase (GDP to GTP or ADP to ATP).
Proline dehydrogenase	ProDH	Proline dehydrogenase (ProDH), L-proline:quinone oxidoreductase, is located on the inner side of the mtIM, oxidizing proline to delta-1-pyrroline-5-carboxylate, with reduction of FAD to FADH₂ and direct entry into the Q-junction, exerting an additive effect of convergent pathways. ProDH is widely distributed in a variety of organisms, is a source of ROS, and may play a role in carcinogenesis.
Prosthetic group		A prosthetic group is a cofactor that is attached permanently and tightly or even covalently to an enzyme and that is regenerated in each enzymatic turnover. Thus a prostethic group is distinguished from a coenzyme or cosubstrate that is attached loosely and transiently. Like a coenzyme, the prosthetic group is required by an enzyme for its activity. A prosthetic group is 'a tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity' (IUPAC definition). FMN/FMNH₂ and FAD/FADH₂ are prosthetic groups of Complex I and Complex II, respectively.
Proton pump		Mitochondrial proton pumps are large enzyme complexes (CI, CIII, CIV, CV) spanning the inner mt-membrane, partially encoded by mtDNA. CI, CIII and CIV are proton pumps that drive protons against the electrochemical protonmotive force, driven by electron transfer from reduced substrates to oxygen. In contrast, ATP synthase (also known as CIV) is a proton pump that utilizes the energy of proton flow along the protonmotive force to drive phosphorylation of ADP to ATP.
Pyruvate carboxylase	PC	Pyruvate carboxylase synthesizes oxaloacetate from pyruvate and CO₂ as an anaplerotic reaction in the mitochondrial matrix of the liver and kidney of higher animals, representing an alternative to the malic enzyme pathway to oxaloacetate or the phosphoenolpyruvate carboxykinase reaction (compare glyoxylate cycle in plants and microorganisms). Carboxylation of pyruvate to oxaloacetate requires Mg-ATP. Acetyl CoA is a strong positive modulator. PC can form pyruvate from oxaloacetate to remove an excess of oxaloacetate which inhibits succinate dehydrogenase.
Pyruvate carrier		The monocarboxylic acid pyruvate^- is exchanged electroneutrally for OH^- by the pyruvate carrier. H⁺/anion symport is equivalent to OH^-/anion antiport.
Pyruvate dehydrogenase	PDH	Pyruvate dehydrogenase is the first component enzyme of the pyruvate dehydrogenase complex, which catalyzes oxidative decarboxylation of pyruvate in the mt-matrix, and yields acetyl-CoA. PDH is known as the mitochondrial gatekeeper in the core energy pathway of electron flow into the tricarboxylic acid cycle.
Pyruvate dehydrogenase complex	PDHC	Oxidative decarboxylation of pyruvate is catalyzed by the pyruvate dehydrogenase complex in the mt-matrix, and yields acetyl-CoA.
P»-system	P»system	The ADP-ATP phosphorylation system or P»-system. See Phosphorylation system.
Q-junction		The Q-junction is a junction for convergent electron flow in the Electron transfer pathway (ET-pathway) from type N substrates and mt-matrix dehydrogenases through Complex I (CI), from type F substrates and FA oxidation through electron-transferring flavoprotein Complex (CETF), from succinate (S) through Complex II (CII), from glycerophosphate (Gp) through glycerophosphate dehydrogenase Complex (CGpDH), from choline through choline dehydrogenase, from dihydro-orotate through dihydro-orotate dehydrogenase, and other enzyme Complexes into the Q-cycle (ubiquinol/ubiquinone), and further downstream to Complex III (CIII) and Complex IV (CIV). The concept of the Q-junction, with the N-junction and F-junction upstream, provides the rationale for defining Electron-transfer-pathway states and categories of SUIT protocols.
Respiratory complexes	CI, CII, CIII, CIV, CETF, CGpDH, ..	Respiratory Complexes are membrane-bound enzymes consisting of several subunits which are involved in energy transduction of the respiratory system. » MiPNet article
Reverse electron flow from CII to CI	RET	Reverse electron flow from CII to CI stimulates production of ROS when mitochondria are incubated with succinate without rotenone in the LEAK state at a high mt-membrane potential. Depolarisation of the mt-membrane potential (e.g. after ADP addition to stimulate OXPHOS) leads to inhibition of RET and therefore, decrease of RET-initiated ROS production. RET can be also measured when mitochondria are respiring using Gp without rotenone in the LEAK state. Addition of I_Q-side inhibitors (ubiquinone-binding side of CI) of CI usually block RET. The following SUIT protocols allow you to measure RET-initiated H₂O₂ flux in mitochondrial preparations: SUIT-009 and SUIT-026.
Sirtuins	Sirt	Sirtuins are NAD⁺-dependent deacetylases which play a prominent role as metabolic regulators. Their dependence on intracellular levels of NAD⁺ (NAD⁺ activates sirtuin activity, whereas NADH inhibits it) makes them suitable as sensors that can detect cellular energy status. » MiPNet article
Succinate dehydrogenase	SDH	Succinate dehydrogenase is a TCA cycle enzyme converting succinate to fumarate while reducing FAD to FADH₂. SDH is the largest component of the mt-inner membrane Complex II (CII) and thus part of the TCA cycle and electron transfer pathway.
Succinate transport		The dicarboxylate carrier catalyses the electroneutral exchange of succinate^2- for HPO_4-^2-.
Succinyl-CoA ligase	SUCLA, SUCLG	Succinyl-CoA ligase (SUCLA or SUCLG) is a TCA cycle enzyme converting succinyl-CoA + ADP or (GDP) + Pi to succinate + ATP (GTP). Two different isoforms exsist: SUCLA (EC: 6.2.1.5) is the ATP-forming isoenzyme, SUCLG (EC: 6.2.1.4) is the GTP-forming isoenzyme. Both reactions are reversible. This reaction is attributed to mitochondrial substrate-level phosphorylation, which is considered as an alternative way of ATP synthesis because it is partially independent from the respiratory chain and from the mitochondrial proton motive force.
Sulfide quinone reductase	SQR	Sulfide quinone reductase (SQR) is involved in electron transfer from sulfide which is used as a hydrogen donor by the mitochondrial respiratory system. SQR is associated with a dioxygenase and a sulfur transferase to release thiosulfate (H₂S₂O₃).
Sulfite oxidase	SO	Sulfite oxidase (SO) is a dimeric enzyme, located in the intermembrane space of mitochondria, with each monomer containing a single Mo cofactor and cyt b5-type heme [1]. SO catalyzes the oxidation of sulfite to sulfate as the terminal step in the metabolism of sulfur amino acids and is vital for human health. Inherited mutations in SO result in severe neurological problems, stunted brain growth, and early death [2]. Function: SO catalyzes the terminal reaction in the oxidative degradation of sulfur amino acids with the formation of a sulfate, electrons pass to cytochrom c and are further utilized in the respiratory system. Sulfite + O₂ + H₂O --> Sulfate + H₂O₂ Localization: The level of expression of SO differs in various tissues with main predominant localization in liver, kidney, skeletal muscle, heart, placenta, and brain in humans and liver, kidney, heart, brain, and lung in rats [3]. Deficiency: SO is vital for metabolic pathways of sulfur amino acids (cysteine and methionine). Complete lack of this enzyme, typically caused by gene mutation, leads to lethal disease called sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy.
Superoxide dismutase	SOD	Mammalian superoxide dismutase (SOD) exists in three forms, of which the Mn-SOD occurs in mitochondria (mtSOD, SOD2; 93 kD homotetramer) and many bacteria, in contrast to the Cu-Zn forms of SOD (cytosolic SOD1, extracellular SOD3 anchored to the extracellular matrix and cell surface). Superoxide anion (O₂^•-) is a major reactive oxygen species (ROS) which is dismutated by SOD to oxygen and H₂O₂.
Thioredoxin reductase	TrxR	Thioredoxin reductase (TrxR) is a family of enzymes able to reduce thioredoxin in mammals.
Tricarboxylate carrier		The tricarboxylate carrier in the inner mt-membrane exchanges malate^2- for citrate^3- or isocitrate^3-, with co-transport of H⁺.

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